Variant report

Variant	rs296733
Chromosome Location	chr9:93754829-93754830
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:93754447-93755155	MCF10A-Er-Src	breast:	n/a	n/a
2	FOSL2	chr9:93754258-93755562	A549	lung:	n/a	n/a
3	SP1	chr9:93754799-93755469	A549	lung:	n/a	n/a
4	CEBPB	chr9:93754796-93755548	HCT-116	colon:	n/a	n/a
5	FOSL1	chr9:93754806-93755545	HCT-116	colon:	n/a	n/a
6	GATA3	chr9:93754754-93755585	SK-N-SH	brain:	n/a	n/a
7	JUN	chr9:93754724-93755355	Hela-S3	cervix:	n/a	n/a
8	GATA3	chr9:93754075-93755660	A549	lung:	n/a	n/a
9	STAT3	chr9:93754469-93755417	MCF10A-Er-Src	breast:	n/a	chr9:93754566-93754577 chr9:93755381-93755392
10	STAT3	chr9:93754382-93755424	MCF10A-Er-Src	breast:	n/a	chr9:93754566-93754577 chr9:93755381-93755392
11	FOS	chr9:93754722-93755441	MCF10A-Er-Src	breast:	n/a	chr9:93755212-93755223
12	NFIC	chr9:93754769-93755462	SK-N-SH	brain:	n/a	n/a
13	EP300	chr9:93754078-93755612	A549	lung:	n/a	n/a
14	MAFK	chr9:93754201-93755390	Hela-S3	cervix:	n/a	chr9:93754230-93754245
15	FOS	chr9:93754396-93755454	MCF10A-Er-Src	breast:	n/a	chr9:93755212-93755223

No.	Distal block	Cell Line	Cell type
1	chr9:93752121..93756766-chr9:93756926..93762091,5	MCF-7	breast:
2	chr9:93748152..93750043-chr9:93753873..93756250,2	MCF-7	breast:
3	chr9:93726945..93729770-chr9:93753086..93755421,2	MCF-7	breast:
4	chr9:93740191..93743980-chr9:93753139..93756785,4	MCF-7	breast:
5	chr9:93699190..93702155-chr9:93754434..93756320,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260454	TF binding region
ENSG00000228216	Chromatin interaction
ENSG00000260454	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs167200	0.88[EUR][1000 genomes]
rs296605	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs296607	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs296608	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs296609	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs296610	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs296640	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs296642	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs296644	0.90[EUR][1000 genomes]
rs296645	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs296646	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs296698	0.99[EUR][1000 genomes]
rs296699	0.99[EUR][1000 genomes]
rs296701	0.99[EUR][1000 genomes]
rs296702	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs296703	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs296714	0.81[EUR][1000 genomes]
rs296715	0.81[EUR][1000 genomes]
rs296716	0.81[EUR][1000 genomes]
rs296717	0.81[EUR][1000 genomes]
rs296721	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs296730	0.99[EUR][1000 genomes]
rs296731	1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs296732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs296734	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs387545	0.84[EUR][1000 genomes]
rs440807	0.84[EUR][1000 genomes]
rs450589	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs70514	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93752400-93755200	Enhancers	Liver	Liver
2	chr9:93753600-93755000	Enhancers	NHDF-Ad	bronchial
3	chr9:93753800-93755000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:93753800-93755000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:93753800-93755000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:93753800-93755000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:93753800-93755000	Enhancers	HMEC	breast
8	chr9:93753800-93755000	Enhancers	NHLF	lung
9	chr9:93753800-93755200	Enhancers	Hela-S3	cervix
10	chr9:93753800-93755200	Enhancers	Osteobl	bone
11	chr9:93753800-93755400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:93753800-93755600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:93753800-93755600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr9:93754000-93755000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:93754000-93755200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr9:93754000-93755200	Enhancers	HSMM	muscle
17	chr9:93754000-93755200	Enhancers	HSMMtube	muscle
18	chr9:93754000-93755600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:93754000-93755600	Enhancers	HUVEC	blood vessel
20	chr9:93754000-93755600	Enhancers	NH-A	brain
21	chr9:93754200-93755000	Enhancers	HepG2	liver
22	chr9:93754200-93755200	Enhancers	NHEK	skin
23	chr9:93754400-93755000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:93754400-93755200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:93754600-93755000	Flanking Active TSS	A549	lung
26	chr9:93754600-93755200	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr9:93754800-93755000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:93754800-93756400	Weak transcription	Adipose Nuclei	Adipose
29	chr9:93754800-93757600	Weak transcription	Colon Smooth Muscle	Colon
30	chr9:93754800-93758000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:93754800-93763400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links